Being a vegetarian I like my pumpkin soup completely free of "body parts" :-) I'ts not an extensive search but I looked at the first 50 hits on google for origins of peter peter pumpkin eater and found no reference to cannibalism...
-- Do not seek to follow in the footsteps of the wise. Seek what they sought. -Basho
Of course, I have no idea what the accurate origin of the rhyme is. I have strong doubts about the chastity belt theory, though, for two reasons. I haven't seen any real evidence that "pumpkin shell" was ever an actual euphemism for a chastity belt. Nor would it explain why Peter is called a "pumpkin eater." Yes, you can draw titillating parallels, but they aren't likely to be correct.
The pumpkin soup story at least seems somewhat based on fact. Pumpkin soup is still sometimes served in a pumpkin shell tureen.
But, really, who cares about factuality here? The real point is to mull over the possibility that a well-known rhyme you heard many times as a child (and perhaps told to your own children) is really a horrific story about a homicidal cuckold who gets revenge on his cheating wife. Stories like that, the ones that leave you with that eerie could-be-true uneasiness, go best with Halloween regardless of the facts. ;-)